Complete Genomic Characterization of Two Beet Soil-Borne Virus Isolates from Turkey: Implications of Comparative Analysis of Genome Sequences

Abstract

Sugar beet (Beta vulgaris L.) is known as a key product for agriculture in several countries across the world. Beet soil-borne virus (BSBV) triggers substantial economic damages to sugar beet by reducing the quantity of the yield and quality of the beet sugars. We conducted the present study to report the complete genome sequences of two BSBV isolates in Turkey for the first time. The genome organization was identical to those previously established BSBV isolates. The tripartite genome of BSBV-TR1 and -TR3 comprised a 5,835-nucleotide (nt) RNA1, a 3,454-nt RNA2, and a 3,005-nt RNA3 segment. According to sequence identity analyses, Turkish isolates were most closely related to the BSBV isolate reported from Iran (97.83-98.77% nt identity). The BSBV isolates worldwide (n = 9) were phylogenetically classified into five (RNA-coat protein read through gene [CPRT], TGB1, and TGB2 segments), four (RNA-rep), or three (TGB3) lineages. In genetic analysis, the TGB3 revealed more genetic variability (Pi = 0.034) compared with other regions. Population selection analysis revealed that most of the codons were generally under negative selection or neutral evolution in the BSBV isolates studied. However, positive selection was detected at codon 135 in the TGB1, which could be an adaptation in order to facilitate the movement and overcome the host plant resistance genes. We expect that the information on genome properties and genetic variability of BSBV, particularly in TGB3, TGB1, and CPRT genes, assist in developing effective control measures in order to prevent severe losses and make amendments in management strategies.

Keywords: beet soil-borne virus; complete genome; phylogenetic analysis; selection pressure; soil-borne virus.

Fig. 1

Necrotic local lesion symptoms on Chenopodium quinoa leaves inoculated with sap from beet soil-borne virus (BSBV)-TR1 infected plants.

Fig. 2

Phylogenetic relationships among sequences of RNA-rep (A), RNA-CPRT (B), TGB1 (C), TGB2 (D), and TGB3 (E) genomic components of beet soil-borne virus (BSBV) inferred by MEGAX using the maximum likelihood method, with 1,000 bootstrap replications and with a 50% bootstrap threshold score. Isolates were indicated in the tree by accession number and geographical origin of collection. Turkish BSBV isolates generated from this study were marked. Potato mop-top virus was used as an outgroup.